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  1. Purely epistatic multi-locus interactions cannot generally be detected via single-locus analysis in case-control studies of complex diseases. Recently, many two-locus and multi-locus analysis techniques have b...

    Authors: Waranyu Wongseree, Anunchai Assawamakin, Theera Piroonratana, Saravudh Sinsomros, Chanin Limwongse and Nachol Chaiyaratana
    Citation: BMC Bioinformatics 2009 10:294
    Content type: Methodology article Published on:

  2. The ability to predict drug sensitivity in cancer is one of the exciting promises of pharmacogenomic research. Several groups have demonstrated the ability to predict drug sensitivity by integrating chemo-sens...

    Authors: Pavithra Shivakumar and Michael Krauthammer
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  3. The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in ...

    Authors: Jonathan L Lustgarten, Shyam Visweswaran, Robert P Bowser, William R Hogan and Vanathi Gopalakrishnan
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  4. Functional magnetic resonance imaging (fMRI) is a technology used to detect brain activity. Patterns of brain activation have been utilized as biomarkers for various neuropsychiatric applications. Detecting de...

    Authors: Bo Jin, Alvin Strasburger, Steven J Laken, F Andrew Kozel, Kevin A Johnson, Mark S George and Xinghua Lu
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  5. The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources. The system's indexing workflow processes the text metadata of dive...

    Authors: Nigam H Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P Chiang and Mark A Musen
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  6. The availability of up-to-date, executable, evidence-based medical knowledge is essential for many clinical applications, such as pharmacovigilance, but executable knowledge is costly to obtain and update. Aut...

    Authors: Xiaoyan Wang, George Hripcsak and Carol Friedman
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  7. Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for trans...

    Authors: Brett R South, Shuying Shen, Makoto Jones, Jennifer Garvin, Matthew H Samore, Wendy W Chapman and Adi V Gundlapalli
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  8. Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to under...

    Authors: Terry H Shen, Christopher S Carlson and Peter Tarczy-Hornoch
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  9. Large repositories of biomedical research data are most useful to translational researchers if their data can be aggregated for efficient queries and analyses. However, inconsistent or non-existent annotations...

    Authors: Erik Pitzer, Ronilda Lacson, Christian Hinske, Jihoon Kim, Pedro AF Galante and Lucila Ohno-Machado
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  10. Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to ...

    Authors: Casey Lynnette Overby, Peter Tarczy-Hornoch and Dina Demner-Fushman
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  11. The decision environment for cancer care is becoming increasingly complex due to the discovery and development of novel genomic tests that offer information regarding therapy response, prognosis and monitoring...

    Authors: Angel Janevski, Sitharthan Kamalakaran, Nilanjana Banerjee, Vinay Varadan and Nevenka Dimitrova
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  12. Current outcome predictors based on "molecular profiling" rely on gene lists selected without consideration for their molecular mechanisms. This study was designed to demonstrate that we could learn about gene...

    Authors: Xinan Yang, Yong Huang, James L Chen, Jianming Xie, Xiao Sun and Yves A Lussier
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  13. The osteocyte is a type of cell that appears to be one of the key endocrine regulators of bone metabolism and a key responder to initiate bone formation and remodeling. Identifying the regulatory networks in o...

    Authors: Angela K Dean, Stephen E Harris, Ivo Kalajzic and Jianhua Ruan
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  14. Physicians use clinical and physiological data to treat patients every day, and it is essential for treating a patient appropriately. However, medical sources of clinical physiological data are only now starti...

    Authors: Adam D Grossman, Mitchell J Cohen, Geoffrey T Manley and Atul J Butte
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  15. Chronic renal diseases are currently classified based on morphological similarities such as whether they produce predominantly inflammatory or non-inflammatory responses. However, such classifications do not r...

    Authors: Suresh K Bhavnani, Felix Eichinger, Sebastian Martini, Paul Saxman, HV Jagadish and Matthias Kretzler
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  16. Identifying disease causing genes and understanding their molecular mechanisms are essential to developing effective therapeutics. Thus, several computational methods have been proposed to prioritize candidate...

    Authors: Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim and Doheon Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  17. Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray appl...

    Authors: Adam M Phillippy, Xiangyu Deng, Wei Zhang and Steven L Salzberg
    Citation: BMC Bioinformatics 2009 10:293
    Content type: Methodology article Published on:

  19. Wiki technology has become a ubiquitous mechanism for dissemination of information, and places strong emphasis on collaboration. We aimed to leverage wiki technology to allow small groups of researchers to col...

    Authors: Jonathan R Manning, Ann Hedley, John J Mullins and Donald R Dunbar
    Citation: BMC Bioinformatics 2009 10:291
    Content type: Software Published on:

  20. The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for ...

    Authors: Marcio L Acencio and Ney Lemke
    Citation: BMC Bioinformatics 2009 10:290
    Content type: Methodology article Published on:

  21. The definition of a hypothetical protein is a protein that is predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation. Hypothetical proteins constit...

    Authors: Claus Desler, Prashanth Suravajhala, May Sanderhoff, Merete Rasmussen and Lene Juel Rasmussen
    Citation: BMC Bioinformatics 2009 10:289
    Content type: Methodology article Published on:

  23. Detecting candidate B-cell epitopes in a protein is a basic and fundamental step in many immunological applications. Due to the impracticality of experimental approaches to systematically scan the entire prote...

    Authors: Nimrod D Rubinstein, Itay Mayrose, Eric Martz and Tal Pupko
    Citation: BMC Bioinformatics 2009 10:287
    Content type: Software Published on:

  24. Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-t...

    Authors: Chao Li, Yuhua Li, Xiangmin Zhang, Phillip Stafford and Valentin Dinu
    Citation: BMC Bioinformatics 2009 10:286
    Content type: Software Published on:

  26. Understanding genome evolution provides insight into biological mechanisms. For many years comparative genomics and analysis of conserved chromosomal regions have helped to unravel the mechanisms involved in g...

    Authors: Virginie Lopez Rascol, Anthony Levasseur, Olivier Chabrol, Simona Grusea, Philippe Gouret, Etienne GJ Danchin and Pierre Pontarotti
    Citation: BMC Bioinformatics 2009 10:284
    Content type: Research article Published on:

  28. The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the an...

    Authors: Matteo Rè, Graziano Pesole and David S Horner
    Citation: BMC Bioinformatics 2009 10:282
    Content type: Methodology article Published on:

  29. Gene discovery algorithms typically examine sequence data for low level patterns. A novel method to computationally discover higher order DNA structures is presented, using a context sensitive grammar. The alg...

    Authors: Guy Tsafnat, Enrico Coiera, Sally R Partridge, Jaron Schaeffer and Jon R Iredell
    Citation: BMC Bioinformatics 2009 10:281
    Content type: Methodology article Published on:

  30. The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of da...

    Authors: Aaron L Vollrath, Adam A Smith, Mark Craven and Christopher A Bradfield
    Citation: BMC Bioinformatics 2009 10:280
    Content type: Software Published on:

  31. Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in or...

    Authors: Johannes Wagener, Ola Spjuth, Egon L Willighagen and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2009 10:279
    Content type: Methodology article Published on:

  33. Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of thes...

    Authors: Wenhui Wang, Juan Nunez-Iglesias, Yihui Luan and Fengzhu Sun
    Citation: BMC Bioinformatics 2009 10:277
    Content type: Research article Published on:

  34. The structural genomics centers provide hundreds of protein structures of unknown function. Therefore, developing methods enabling the determination of a protein function automatically is imperative. The deter...

    Authors: Joachim Giard, Jérôme Ambroise, Jean-Luc Gala and Benoît Macq
    Citation: BMC Bioinformatics 2009 10:276
    Content type: Research article Published on:

  35. The analysis of high-throughput gene expression data with respect to sets of genes rather than individual genes has many advantages. A variety of methods have been developed for assessing the enrichment of set...

    Authors: Luca Abatangelo, Rosalia Maglietta, Angela Distaso, Annarita D'Addabbo, Teresa Maria Creanza, Sayan Mukherjee and Nicola Ancona
    Citation: BMC Bioinformatics 2009 10:275
    Content type: Research article Published on:

  36. Knowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous...

    Authors: Torsten Blum, Sebastian Briesemeister and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2009 10:274
    Content type: Software Published on:

  37. Enzymes that depend on vitamin B6 (and in particular on its metabolically active form, pyridoxal 5'-phosphate, PLP) are of great relevance to biology and medicine, as they catalyze a wide variety of biochemica...

    Authors: Riccardo Percudani and Alessio Peracchi
    Citation: BMC Bioinformatics 2009 10:273
    Content type: Database Published on:

  38. Joint analysis of transcriptomic and proteomic data taken from the same samples has the potential to elucidate complex biological mechanisms. Most current methods that integrate these datasets allow for the co...

    Authors: Chuen Seng Tan, Agus Salim, Alexander Ploner, Janne Lehtiö, Kee Seng Chia and Yudi Pawitan
    Citation: BMC Bioinformatics 2009 10:272
    Content type: Research article Published on:

  39. Promoter identification is a first step in the quest to explain gene regulation in bacteria. It has been demonstrated that the initiation of bacterial transcription depends upon the stability and topology of D...

    Authors: Ronna R Mallios, David M Ojcius and David H Ardell
    Citation: BMC Bioinformatics 2009 10:271
    Content type: Research article Published on:

  40. Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments...

    Authors: Mônica G Campiteli, Frederico M Soriani, Iran Malavazi, Osame Kinouchi, Carlos AB Pereira and Gustavo H Goldman
    Citation: BMC Bioinformatics 2009 10:270
    Content type: Methodology article Published on:

  41. Global partitioning based on pairwise associations of SNPs has not previously been used to define haplotype blocks within genomes. Here, we define an association index based on LD between SNP pairs. We use the...

    Authors: Ali Katanforoush, Mehdi Sadeghi, Hamid Pezeshk and Elahe Elahi
    Citation: BMC Bioinformatics 2009 10:269
    Content type: Methodology article Published on:

  42. The reaction of HIV protease to inhibitor therapy is characterized by the emergence of complex mutational patterns which confer drug resistance. The response of HIV protease to drugs often involves both primar...

    Authors: Omar Haq, Ronald M Levy, Alexandre V Morozov and Michael Andrec
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  43. Linking structural effects of mutations to functional outcomes is a major issue in structural bioinformatics, and many tools and studies have shown that specific structural properties such as stability and res...

    Authors: Joke Reumers, Joost Schymkowitz and Fréderic Rousseau
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  44. Mutations resulting in the disruption of protein function are the underlying causes of many genetic diseases. Some mutations affect the number of expressed proteins while others alter the activity on a per-mol...

    Authors: Yana Bromberg and Burkhard Rost
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  45. Human mitochondrial DNA (mtDNA) variations have been implicated in a broad spectrum of diseases. With over 3000 mtDNA variations reported across databases, establishing pathogenicity of variations in mtDNA is ...

    Authors: Anshu Bhardwaj, Mitali Mukerji, Shipra Sharma, Jinny Paul, Chaitanya S Gokhale, Achal K Srivastava and Shrish Tiwari
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  46. Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understandin...

    Authors: Anna Bauer-Mehren, Laura I Furlong, Michael Rautschka and Ferran Sanz
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  47. The phenotypic effects of sequence variations in protein-coding regions come about primarily via their effects on the resulting structures, for example by disrupting active sites or affecting structural stabil...

    Authors: Jose MG Izarzugaza, Anja Baresic, Lisa EM McMillan, Corin Yeats, Andrew B Clegg, Christine A Orengo, Andrew CR Martin and Alfonso Valencia
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  48. A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Ex...

    Authors: Kevin Nagel, Antonio Jimeno-Yepes and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  49. A better understanding of the mechanisms of an enzyme's functionality and stability, as well as knowledge and impact of mutations is crucial for researchers working with enzymes. Though, several of the enzymes...

    Authors: Süveyda Yeniterzi and Uğur Sezerman
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

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